Merge pull request #41 from xchem/docs_dev

Move things to readthedocs

Author: mwinokan

.gitignore

@@ -19,3 +19,5 @@ build
 *~
 \#*#
 \#*
+
+.DS_Store

README.md

@@ -12,9 +12,9 @@ Tools to generate data suitable for loading into [Fragalysis](https://fragalysis
 This supersedes [Fragalysis-API](https://github.com/xchem/fragalysis-api).
 
 See:
-* [User Guide](USER-GUIDE.md)
-* [Developer Guide](DEV-GUIDE.md)
-* [Algorithm Guide](ALGORITHM-GUIDE.md)
+* [User Guide](https://xchem-align.readthedocs.io/en/latest/USER-GUIDE.md)
+* [Developer Guide](https://xchem-align.readthedocs.io/en/latest/DEV-GUIDE.md)
+* [Algorithm Guide](https://xchem-align.readthedocs.io/en/latest/ALGORITHM-GUIDE.md)
 
 Contributors:
 * Tim Dudgeon (Informatics Matters)

ALGORITHM-GUIDE.md docs/source/ALGORITHM-GUIDE.md

@@ -10,12 +10,12 @@ _XChemAlign_ is a small suite of tools for preparing PDB models for loading into
 ## Overview
 
 There are a few steps involved.
-1. [**Enable**](#1-enabling-the-xchemalign-environment) the XChemAlign environment
-2. [**Declare**](#2-declaring-things) a few things about your data in two structured files in `yaml`[^1]
-3. [**Collate**](#3-collating-files) your files in a new (specific) directory structure
-4. [**Align**](#4-aligning-everything) all binding sites to common origins
-5. [**Release**](#5-upload-to-fragalysis) the data to Fragalysis
-6. [**Re-release**](#6-creating-subsequent-versions) additional data
+1. [**Enable**](#enabling-the-xchemalign-environment) the XChemAlign environment
+2. [**Declare**](#declaring-things) a few things about your data in two structured files in `yaml`[^1]
+3. [**Collate**](#collating-files) your files in a new (specific) directory structure
+4. [**Align**](#aligning-everything) all binding sites to common origins
+5. [**Release**](#upload-to-fragalysis) the data to Fragalysis
+6. [**Re-release**](#creating-subsequent-versions) additional data
 
 If you won't run this at Diamond, you will first have to set up your environment and copy over files. See the [instructions here](#non-diamond-instructions)
 

DEV-GUIDE.md docs/source/DEV-GUIDE.md

@@ -1,4 +1,28 @@
 
 # XChem Align
 
-Placeholder file for XCHem Align documentation root.
+![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/xchem/xchem-align?include_prereleases)
+
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+[![test](https://github.com/xchem/xchem-align/actions/workflows/test.yaml/badge.svg)](https://github.com/xchem/xchem-align/actions/workflows/test.yaml)
+[![mypy](https://github.com/xchem/xchem-align/actions/workflows/mypy.yaml/badge.svg)](https://github.com/xchem/xchem-align/actions/workflows/mypy.yaml)
+
+Tools to generate data suitable for loading into [Fragalysis](https://fragalysis.diamond.ac.uk/).
+
+This supersedes [Fragalysis-API](https://github.com/xchem/fragalysis-api).
+
+See:
+
+```{toctree}
+:maxdepth: 1
+USER-GUIDE.md
+DEV-GUIDE.md
+ALGORITHM-GUIDE.md
+```
+
+Contributors:
+* Tim Dudgeon (Informatics Matters)
+* Conor Wild (Diamond)
+* Alan Christie (Informatics Matters)
+* Kalev Takis (Informatics Matters)